• XDS may be invoked directly by typing xds. However, you will have to provide input files. Therefore, a script called autoxds has been provided that will automatically generate the necessary input files and start up XDS. To invoke the autoxds script to process all images in a directory just type "autoxds imagefile.img" If you only want to process a given number of frames you would type "autoxds imagefile.img max_frames"
  • Here is an example of an input file generated by autoxds: XDS.INP
• AutoXDS
  • usage: autoxds any_frame [max_frames]
  • AutoXDS is a script that was written by Michel Fodje that automatically generates the input files that XDS requires and then invokes XDS. Although, AutoXDS is intended to automate the generation of the input files the user should familiarize themselves with XDS to take full advantage of its features. In particular, there may be some instances when the user would like XDS to try a different Spacegroup than the one generated by AutoXDS. For example here is a list of XDS: Input Parameters.
  • Autoprocess
    • autoprocess [options] /path/to/set1.img /path/to/set2.img ... /path/to/setn.img
      
      options:
      --mad, -m : Process each set, scale together and generate separate reflection files.
      --screen, -s : Process a few frames from characterize crystal from each set.
      --anom, -a : Process with Friedel's law False
      --prefix=p1,p2,p3 : comma separated list of prefixes to use for output files.
      Default 1,2,3,...,n
      prefix order should correspond to the order of the data sets
      for example for MAD data, use --prefix=peak,infl,remo
      --dir=/path : Directory to store processed results. Subdirectories will be created inside.
      Default current directory.
      --help, -h : display this message
      Default (no option): Process each set, scale together and merge into one reflection file.
      
      data sets:
      Each data set can be represented by any frame from that set.
       
    • Autoprocess is another script that was written by Michel Fodje that automatically generates the input files that XDS requires and then invokes XDS. Although, AutoXDS is intended to automate the generation of the input files the user should familiarize themselves with XDS to take full advantage of its features.

     

• Start HKL2000 by typing HKL2000.
• If you are running HKL2000 off site for data collected at the CMCF, you will need the site file here: def.site (for MarCCD 300), def.site (for MarCCD 225)
• As described on its website: "HKL-2000 program package is based on the extended versions of Denzo, XDisplayF and Scalepack. It consists of several subprograms coordinated by the graphical command center. The most important new elements are: strategy and simulation, 3-D processing, mosaicity refinement during processing, variable spot size, easy change of the space group, report generation, etc."
• For details on the usage of HKL2000 please check out the online HKL2000 Manual.

• Start mosflm by typing ipmosflm. For details on the usage of mosflm please see the MOSFLM 7.0.4 User Guide.
• You can start the new mosflm GUI by typing imosflm.
• Mosflm may be used to integrate your diffraction data obtained at the CMCF from the marmosaic225 area detector.

• "The CCP4 program suite is a collection of disparate programs covering most of the computations required for macromolecular crystallography. They have been collected and developed under the auspices of the Collaborative Computing Project Number 4, in Protein Crystallography."
• The graphical user interface is started by typing ccp4i .

• Automated structure solution for MAD and MIR. Input files
• SOLVE scripts here.
• Just about anything that SOLVE/RESOLVE scripts can do, PHENIX can do (better)! Give it a try !

• PHENIX is a new software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods. The PHENIX system also includes SOLVE/RESOLVE, Phaser, Textal, the CCI Applications (phenix.xtriage, phenix.refine, elbow and many more), components from Molprobity, and the Computational Crystallography Toolbox in a Python framework. The Phenix platform allows to perform different phases of structure solution and can be used either from a command line interface (link) or through a graphical user interface (GUI).

• Current tasks and strategies available include:  

  • Density modification: carries out a single run of RESOLVE
  • Substructure solution: runs phenix.hyss
  • Molecular replacement: computes rotation and translation functions with PHASER
  • Model building: using TEXTAL or RESOLVE
  • Ligand identification: Using RESOLVE

• Just about anything that SOLVE/RESOLVE scripts can do, PHENIX can do (better)! Give it a try. 

• To run the PHENIX Graphical Interface, type phenix &

• Additional documentation files for running Phenix can be found in the Running Phenix section of the online Phenix documentation.

.

• SHELX is a set of programs for crystal structure determination from single-crystal diffraction data. The suite consists of the following programs:

  • SHELXS: Structure solution by Patterson and direct methods
  • SHELXC: Preparations of files for macromolecular phasing with SHELXD and SHELXE
  • SHELXD: Structure solution for difficult problems (and location of heavy atom sites)
  • SHELXE: Phases from SHELXD heavy atom sites (and density modification)
  • SHELXL: Structure refinement (use SHELXH for large structures)
  • CIFTAB: Tables for publication via (small molecule) CIF format
  • SHELXA: Post-absorption corrections (for emergency use only)
  • SHELXPRO: Protein interface to SHELX
  • SHELXWAT: Automatic water divining for macromolecules

  The new program SHELXC is designed to provide a simple and fast way of setting up the files for the programs SHELXD (heavy atom location) and SHELXE (phasing and density modification) that are used for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods.

  SHELXC reads HKL2000 .sca files. To transfer data from CCP4 it is advisable to generate .sca files using CCP4i.

  Examples of input files for MAD, SAD, SIR or SIRAS structure solution can be found on any of the beamline computing stations (opi1608-001, 002, 003) in /opt/cmcf_apps/shelx/input-files or  at http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/SHELX_C/D/E .

  View the SHELX online Manual here.

• Crystallography & NMR System (CNS) has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Highlights for X-ray crystallography include heavy atom searching, experimental phasing (including MAD and MIR), density modification, and crystallographic refinement with maximum likelihood targets.

  Input files and manual here or on any of the beamline workstations in /opt/cmcf_apps/cns_solve_1.2/inputs .

• Coot is a molecular graphics program for model building, model completion and validation. Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots. The program is available on any of the beamline workstations.

  View the Coot manual here.